Well Chameleon Coating and Signature Masking (can't remember if that's what it's called in SR4A) could go a long way to keep the craft unnoticed by local law enforcement. As far as legality, corporations can usually license things that individuals cannot, and its usually much easier for them to license things that individuals can (Look at getting a class III license in Missouri, it is far easier to pay $100 and get it under a business license than to get it individually). S-K does have a private "army" so I would see them being licensed to have military vehicles that could (with permissions) travel through local airspace in UCAS (much like PMC vehicles).
As far as the vehicle to use, the main question is what is the goal of the vehicle? If it is just an insertion vehicle then something small, light and fast would work just fine. If it's meant to be the vehicle always used despite the job, I'd recommend something a bit larger in case they have to bring something back.
As far as suggestions:
GMC Banshee (Big and very fast. Rename it if you want a S-K feel since Ares owns GMC)
Ares Dragon (Utility chopper, easily modifiable, but can look inconspicuous enough)
HAWKER-SIDDLEY HS-895 Skytruck (Big cargo plane, more noticeable than the dragon though)
ARES TR-55 (Smaller transport plane)
EUROCOPTER TIGER (Standard Assault Helicopter, it would be small and a tight fit, but may work)
SAEDER-KRUPP LAKOTA (A Small Cargo Helicopter, could be refitted easily to be more compatible with the needs)
My personal choice would be along these lines:
S-K Nightshade (Nachtschatten if you prefer the German)
[Military Grade Recon and Skirmish VTOL]
Handling: +1
Accel: 50/250
Speed: 1000
Pilot: 6 (15,000¥)
Body: 20
Armor: 20
Sensor: 6
Cost: 2,448,175¥
Slots: 0
Stock Mods:
Ext. Reinforced Flexible Remote Weapon Mount x2 (13,000¥)
Ext. Normal Flexible Remote Weapon Mount x3 (12,000¥)
Modifications:
Chameleon Coating [2 Slots] (20,000¥)
Signature Masking 6 [6 Slots] (12,000¥)
Armor 20 [1 Slot ] ( 4,000¥)
Enhanced Rigger Cacoon [2 Slots] ( 4,000¥)
Personal Armor 10 [2 Slots] ( 5,000¥)
Smoke Projector [1 Slot ] ( 700¥)
Small Landing Drone Rack x 2 [6 Slots] (10,000¥)
Sensors:
• Atmosphere Sensor Rating 3 [1 Capacity] ( 75¥)
• 2 Cameras Rating 6 [2 Capacity] ( 1,200¥)
• 2 Laser Range Finders [2 Capacity]
• 2 Motion Sensors [2 Capacity]
• Radar Rating 6 [5 Capacity] ( 1,200¥)
With chameleon coating, everyone trying to Perceive the vehicle visually is at a -4.
With Signature Masking, any attempts to use a sensor to find the vehicle suffers a penalty equal to -6 or -sensor rating (whichever is lower).